At the center of the issues lies with the way the school get founded. Every school, government or independent, get the same amount of money per student. However, government run schools and independent school have different requirement and regulations, which unsurprisingly leads to issues. Independent school are not outsourced education where the government issues the requirements and pays the bills. Government pays the pill and then the idea is that the students (children) are the ones that should issue requirements and thus move if they feel the school is not serving them.
Government run schools must exist and be located to serve everyone in society, including students that on average cost more than other students. Government schools must also over-allocate space so that changes in population can still be managed. Government run schools can not be secular, and in practice unable to reject students.
On top of this there are critique of rampant corruption and fraudulent grades given to students, both which looks quite bad when dealing with government money. In one case there was also connection to terrorism and IS funding.